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Human p38 MAP kinase in complex with NP-F3 and RL87
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM MES, pH 6.5, 19-24% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.13 α = 90 b = 74.31 β = 90 c = 77.75 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL PSI PILATUS 6M Dynamical bendable mirrors 2011-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 45 99.8 0.033 30.4 6.18 20076 20045 -3 53.958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 100 0.165 9.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZYJ 2.5 45 20076 20045 956 99.8 0.2337 0.2266 0.2816 0.3174 0.264 RANDOM 40.3721
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.91 -0.8 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_3_deg 21.248 r_dihedral_angle_4_deg 17.039 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.133 r_scbond_it 1.873 r_angle_refined_deg 1.531 r_mcangle_it 1.497 r_mcbond_it 0.786 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_3_deg 21.248 r_dihedral_angle_4_deg 17.039 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.133 r_scbond_it 1.873 r_angle_refined_deg 1.531 r_mcangle_it 1.497 r_mcbond_it 0.786 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2699 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 35
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling